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Cineplex editor

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The CinePlex Editor is a software tool designed for reviewing and editing video recordings. It allows users to view synchronized video and electrophysiology data, and make annotations or adjustments to the recordings.

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Lab products found in correlation

Cineplex studio, by Plexon (5 mentions) Omniplex d neural acquisition system, by Plexon (2 mentions) Offline sorter v3, by Plexon (2 mentions) Cineplex software, by Plexon (1 mentions) Matlab, by MathWorks (1 mentions)

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CinePlex (12 citations) CinePlex Editor software (4 citations)

8 protocols using cineplex editor

1

Multimodal Unit Isolation Protocol

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Spikes were assigned to individual units by offline manual clustering of waveform characteristics (valley amplitude, peak-valley, energy, principal components, and waveform width at half max). Tetrode localization was performed using histology, and further guided by the LFP theta amplitude and phase, and sharp-wave ripple amplitude. Only well-isolated units (Isolation Rating > 40 L-Ratio <0.001) were kept for further analysis. Behavior was monitored from an overhead camera and a second camera with a close-up view of the test pots (see above). Door movements, and treadmill onset and offset were automatically strobed into the recording amplifier. Test object sampling events were hand-coded using CinePlex editor (Plexon) using video taken at 30 Hz from the camera trained on the reward objects.
Cao R., Bladon J.H., Charczynski S.J., Hasselmo M.E, & Howard M.W. (2022). Internally generated time in the rodent hippocampus is logarithmically compressed. eLife, 11, e75353.
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2

Open Field Habituation Locomotor Assessment

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Open field habituation task was performed in a 40 × 40 × 40 cm3 box during 2 × 15-min habituation sessions, spaced 1–2 h apart. Animals at 8–12 weeks of age were placed in the behavior box and allowed to explore freely during each habituation session. Sessions were recorded and locomotor activity was tracked using Plexon’s CinePlex Studio and analyzed using Plexon’s CinePlex Editor and code written in MATLAB. For analysis, the box was divided into two zones: an ‘inner’ zone (containing the inner 30 × 30 cm2 center square) and an ‘outer’ zone (the outermost area 5 cm from the walls). Total distance traveled was computed as the sum of distance covered over the course of each habituation session.
Stoppel L.J., Kazdoba T.M., Schaffler M.D., Preza A.R., Heynen A., Crawley J.N, & Bear M.F. (2017). R-Baclofen Reverses Cognitive Deficits and Improves Social Interactions in Two Lines of 16p11.2 Deletion Mice. Neuropsychopharmacology, 43(3), 513-524.
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3

Extracellular Recordings and Position Tracking

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Extracellular recordings from custom tetrodes were recorded by a OmniPlex D Neural Acquisition System (Plexon). Each channel was amplified and bandpass filtered (154 Hz–8.8 kHz) to obtain both single-unit spike activity and LFPs (1.5 Hz–400 Hz). Spike channels were locally referenced to remove both movement-related noise and potential electrical noise. Spikes were detected via threshold crossing and digitized at 40 kHz. To isolate single-units, waveform clusters from all four electrodes within a tetrode were manually identified using the Offline Sorter v3 (Plexon). Cineplex Studio (Plexon) was used for capturing animal location data via three infrared LEDs positioned atop the surgically implanted microdrive. Cineplex Editor (Plexon) was employed offline to enter event markers and to verify animal position data.
Hennager D.J., Ikuma M., Hoshi T, & Welsh M.J. (2001). A conditional probability analysis of cystic fibrosis transmembrane conductance regulator gating indicates that ATP has multiple effects during the gating cycle. Proceedings of the National Academy of Sciences of the United States of America, 98(6), 3594-3599.
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4

Social Interaction Preference Assay

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In this test, we placed plexiglass barriers at the end of the Goal arms to create 2 social chambers for the presentation of stimulus animals. Interactions between the test mouse and the stimulus animals were possible through holes in the barriers. The test subject was acclimatized to the T maze for 10 min. In this epoch, the social chambers were empty. After acclimatization, the animal was briefly enclosed in the Start arm, the first stimulus animal was randomly placed in one of the social chambers, and the test subject was allowed to re-explore the maze for 10 min. After another brief enclosure, the second stimulus animal was placed in the remaining social chamber, and the test subject re-explored the maze for 10 min. The session ended with a final 10 min epoch similar to the acclimatization period and a subsequent 10 min post-behavior epoch in the recording cage, before disconnecting the headgear. For each test mouse, we computed the time spent in each compartment using CinePlex Editor (Plexon).
Ferreira-Fernandes E., Laranjo M., Reis T., Canijo B., Ferreira P.A., Martins P., Vilarinho J., Tavakoli M., Kunicki C, & Peça J. (2023). In vivo recordings in freely behaving mice using independent silicon probes targeting multiple brain regions. Frontiers in Neural Circuits, 17, 1293620.
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5

Behavioural Tracking and Freezing Analysis

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All behavioural sessions were recorded using an overhead camera (Stingray, Allied Vision) and Cineplex software (Plexon) at 40 Hz. Mice were tracked using contour tracking, and freezing behaviour was automatically scored with the assistance of a frame-by-frame analysis of pixel change (Cineplex Editor, Plexon). Freezing behaviour minimum duration threshold was set to 2 s. Automatically detected freezing epochs were manually inspected on the video recording to eliminate false-positive and false-negative freezing bouts (e.g., during micro-grooming episodes or due to motion artefacts caused by cable movement, respectively). Annotated freezing data were then temporally aligned with miniscope imaged data and finally downsampled to 10 Hz.
Hagihara K.M., Bukalo O., Zeller M., Aksoy-Aksel A., Karalis N., Limoges A., Rigg T., Campbell T., Mendez A., Weinholtz C., Mahn M., Zweifel L.S., Palmiter R.D., Ehrlich I., Lüthi A, & Holmes A. (2021). Intercalated amygdala clusters orchestrate a switch in fear state. Nature, 594(7863), 403-407.
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6

Behavioral Effects of MK-801 and Modulators

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To determine the effects of genotype on MK-801–induced hyperlocomotion, mice were habituated in the open field (40 cm by 40 cm by 40 cm box) for 60 min, followed by the administration of vehicle or MK-801, and locomotor activity was recorded for another 60 min. To determine the effects of MTEP and BRD0705 on MK-801–induced hyperlocomotion, mice were habituated in the open field for 30 min, followed by the intraperitoneal administration of MTEP (10 mg/kg at a dosing volume of 10 ml/kg) or BRD0705 (30 mg/kg at a dosing volume of 2 ml/kg). After an additional 30 min, MK-801 (0.3 mg/kg at a dosing volume of 10 ml/kg) was administered intraperitoneally, and locomotor activity was recorded for another 60 min. The time course of drug-induced changes in ambulation was expressed as centimeters traveled per 5 min over the 120-min session. Sessions were recorded using Plexon’s CinePlex Studio and analyzed using Plexon’s CinePlex Editor and code was written in MATLAB. MK-801–induced locomotor activity was scored and analyzed using the average of the final 5 min (minutes 115 to 120) of observation per cohort.
McCamphill P.K., Stoppel L.J., Senter R.K., Lewis M.C., Heynen A.J., Stoppel D.C., Sridhar V., Collins K.A., Shi X., Pan J.Q., Madison J., Cottrell J.R., Huber K.M., Scolnick E.M., Holson E.B., Wagner F.F, & Bear M.F. (2020). Selective inhibition of glycogen synthase kinase 3α corrects pathophysiology in a mouse model of fragile X syndrome. Science translational medicine, 12(544), eaam8572.
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7

Electrophysiological Recordings and Neural Tracking

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Electrophysiological recordings for this project were collected using a 96 channel OmniPlex D Neural Acquisition System (Plexon). Each channel was amplified and bandpass filtered for both single-unit activity (154 Hz to 8.8 kHz) and local field potentials (1.5 Hz to 400 kHz). Spike channels were referenced to a local electrode in the same region in order to remove both movement-related and any electrical noise. Action potentials of neurons were detected via threshold crossing and digitized at 40 kHz. Between recorded training sessions tetrodes were advanced based on visual inspection, in order to maximize neural unit yield, and allowed to settle overnight before conducting the next recording session. Individual neural units were isolated via manual offline clustering, employing Offline Sorter v3 (Plexon). Cineplex Studio (Plexon) was used for capturing behavioral tracking data via three infrared LEDs positioned atop the microdrive EIB. Cineplex Editor (Plexon) was employed to enter event markers and to verify animal positional tracking data.
Sheehan D.J., Charczynski S.J., Fordyce B.A., Hasselmo M.E., & Howard M.W. (2021). “A compressed representation of spatial distance in the rodent hippocampus’’.
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8

Auditory Fear Conditioning in Mice

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Nine days after choleratoxin-B injection to mPFC subdivisions, mice were submitted to an auditory fear conditioning paradigm. Five pairings of auditory conditioned stimulus (CS) and aversive unconditioned stimulus (US) were presented with an intertrial interval of 78-110 s. The CS consisted of 50 ms pips repeated at 0.9 Hz (total duration of 30 s) with a pip frequency of 7.5 kHz and 75 dB sound pressure level (Tucker-Davis Technologies) and was followed by a 1 s 0.65 mA AC foot shock (Coulbourn Instruments). Freezing behavior was classified as a 2 s absence of movement and quantified using Cineplex Studio and CinePlex Editor video tracking software (Plexon) and customwritten MATLAB (MathWorks) routines. Mice were perfused for immunohistochemical analysis 24 hr after fear conditioning.
Vogel E., Krabbe S., Gründemann J., Wamsteeker Cusulin J.I, & Lüthi A. (2016). Projection-Specific Dynamic Regulation of Inhibition in Amygdala Micro-Circuits. Neuron, 91(3).
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